setwd("~/Postgrad/Honours")
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(survival)
Load cohort data:
load('brca2116_dataset.RData')
Two objects:
expDat: normalised gene expression data (on log scale) from 2116 tumours Affymetrix arrays). Probe data have been collapsed to 12403 genes (gene symbols used as IDs).sampleData: data relating to each sample:
HIgh or low IQSEC2 include ER+ and ER- samples:
sampleDatap = sampleData[(sampleData$ER.status=="ER+" & sampleData$EndocrineTrt==1) ,]
sampleDatan = sampleData[(sampleData$ER.status=="ER-" & sampleData$PgR.status=="PgR-" & sampleData$EndocrineTrt==1),]
dim(sampleData[sampleData$ER.status=="ER-" & sampleData$PgR.status=="PgR-",])
## [1] 630 17
sampleDataop = filter(sampleDatap, rowSums(is.na(sampleDatap)) != ncol(sampleDatap))
sampleDataon = filter(sampleDatan, rowSums(is.na(sampleDatan)) != ncol(sampleDatan))
expDatop = expDat[,sampleDataop$sampleNames]
expDaton = expDat[,sampleDataon$sampleNames]
IQSEC2pif = ifelse( expDatop["IQSEC2",] > mean(expDatop["IQSEC2",]), 1, 0)
table(IQSEC2pif)
## IQSEC2pif
## 0 1
## 439 352
plot( survfit( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ IQSEC2pif ),
xlab = "Time in months", ylab = "Metastasis-free survival", col = c(2,4))
legend('topright', c("IQSEC2 high", "IQSEC2 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~IQSEC2pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## IQSEC2pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## IQSEC2pif=0 315 73 84.2 1.48 3.39
## IQSEC2pif=1 267 77 65.8 1.89 3.39
##
## Chisq= 3.4 on 1 degrees of freedom, p= 0.07
IQSEC2nif = ifelse( expDaton["IQSEC2",] > mean(expDaton["IQSEC2",]), 1, 0)
table(IQSEC2nif)
## IQSEC2nif
## 0 1
## 19 23
plot( survfit( Surv(sampleDataon$dmfsTime, sampleDataon$dmfsEvent) ~ IQSEC2nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IQSEC2 high", "IQSEC2 low"), fill = c('red', 'blue'))
for (i in 1:15){
boxplot(expDatop["IQSEC2",i])
}
CDpif = ifelse( expDatop["CD163",] > median(expDatop["CD163",]), 1, 0)
table(CDpif)
## CDpif
## 0 1
## 398 393
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CDpif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("CD163 high", "CD163 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~CDpif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~
## CDpif)
##
## n=773, 18 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## CDpif=0 388 81 84.6 0.152 0.301
## CDpif=1 385 92 88.4 0.146 0.301
##
## Chisq= 0.3 on 1 degrees of freedom, p= 0.6
CDnif = ifelse( expDaton["CD163",] > median(expDaton["CD163",]), 1, 0)
table(CDnif)
## CDnif
## 0 1
## 21 21
plot( survfit( Surv(sampleDataon$dmfsTime, sampleDataon$dmfsEvent) ~ CDnif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("CD high", "CD low"), fill = c('red', 'blue'))
HIST1H2AJpif = ifelse( expDatop["HIST1H2AJ",] > mean(expDatop["HIST1H2AJ",]), 1, 0)
table(HIST1H2AJpif)
## HIST1H2AJpif
## 0 1
## 424 367
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dfsEvent) ~ HIST1H2AJpif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("HIST1H2AJ high", "HIST1H2AJ low"), fill = c('red', 'blue'))
HIST1H2AJnif = ifelse( expDaton["HIST1H2AJ",] > mean(expDaton["HIST1H2AJ",]), 1, 0)
table(HIST1H2AJnif)
## HIST1H2AJnif
## 0 1
## 23 19
plot( survfit( Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~ HIST1H2AJnif ),
xlab = "Time in months", ylab = "Recurrence-free survival proportion", col = c(2,4))
legend('topright', c("HIST1H2AJ high", "HIST1H2AJ low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~HIST1H2AJnif )
## Call:
## survdiff(formula = Surv(sampleDataon$dfsTime, sampleDataon$dfsEvent) ~
## HIST1H2AJnif)
##
## n=25, 17 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## HIST1H2AJnif=0 15 4 6.34 0.864 2.38
## HIST1H2AJnif=1 10 6 3.66 1.497 2.38
##
## Chisq= 2.4 on 1 degrees of freedom, p= 0.1
CXCL13pif = ifelse( expDatop["CXCL13",] > mean(expDatop["CXCL13",]), 1, 0)
table(CXCL13pif)
## CXCL13pif
## 0 1
## 500 291
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CXCL13pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CXCL13 high", "CXCL13 low"), fill = c('red', 'blue'))
CXCL13nif = ifelse( expDaton["CXCL13",] > mean(expDaton["CXCL13",]), 1, 0)
table(CXCL13nif)
## CXCL13nif
## 0 1
## 18 24
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CXCL13nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CXCL13 high", "CXCL13 low"), fill = c('red', 'blue'))
CXCL13nif
## GSM79117 GSM79148 GSM79191 GSM79195 GSM79239 GSM79259 GSM79274
## 1 1 1 1 1 0 0
## GSM79292 GSM79341 GSM79351 GSM107082 GSM107131 GSM107166 GSM107183
## 1 1 1 1 1 0 1
## OXF5431 OXF5432 OXF5440 OXF5444 OXF5448 OXF5451 OXF5460
## 0 0 0 0 1 0 1
## OXF5466 GSM50045 GSM50048 GSM50054 GSM50060 GSM50061 GSM50066
## 1 0 0 1 1 1 0
## GSM50071 GSM50093 GSM50116 1639356696 1639355859 1639356632 1639357580
## 0 0 0 0 1 1 1
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162
## 0 1 1 1 1 0 0
STX8pif = ifelse( expDatop["STX8",] > mean(expDatop["STX8",]), 1, 0)
table(STX8pif)
## STX8pif
## 0 1
## 393 398
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ STX8pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("STX8 high", "STX8 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~STX8pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## STX8pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## STX8pif=0 287 78 74.4 0.177 0.352
## STX8pif=1 295 72 75.6 0.174 0.352
##
## Chisq= 0.4 on 1 degrees of freedom, p= 0.6
STX8nif = ifelse( expDaton["STX8",] > mean(expDaton["STX8",]), 1, 0)
table(STX8nif)
## STX8nif
## 0 1
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ STX8nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("STX8 high", "STX8 low"), fill = c('red', 'blue'))
TIMM22pif = ifelse( expDatop["TIMM22",] > mean(expDatop["TIMM22",]), 1, 0)
table(TIMM22pif)
## TIMM22pif
## 0 1
## 420 371
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ TIMM22pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("TIMM22 high", "TIMM22 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~TIMM22pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## TIMM22pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## TIMM22pif=0 311 84 78.7 0.360 0.759
## TIMM22pif=1 271 66 71.3 0.397 0.759
##
## Chisq= 0.8 on 1 degrees of freedom, p= 0.4
TIMM22nif = ifelse( expDaton["TIMM22",] > mean(expDaton["TIMM22",]), 1, 0)
table(TIMM22nif)
## TIMM22nif
## 0 1
## 25 17
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ TIMM22nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("TIMM22 high", "TIM22 low"), fill = c('red', 'blue'))
ARHGEF7pif = ifelse( expDatop["ARHGEF7",] > mean(expDatop["ARHGEF7",]), 1, 0)
table(ARHGEF7pif)
## ARHGEF7pif
## 0 1
## 378 413
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ ARHGEF7pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("ARHGEF7 high", "ARHGEF7 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~ARHGEF7pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## ARHGEF7pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## ARHGEF7pif=0 273 77 66 1.82 3.27
## ARHGEF7pif=1 309 73 84 1.43 3.27
##
## Chisq= 3.3 on 1 degrees of freedom, p= 0.07
ARHGEF7nif = ifelse( expDaton["ARHGEF7",] > mean(expDaton["ARHGEF7",]), 1, 0)
table(ARHGEF7nif)
## ARHGEF7nif
## 0 1
## 19 23
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ ARHGEF7nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("ARHGEF7 high", "ARHGEF7 low"), fill = c('red', 'blue'))
MKRN2pif = ifelse( expDatop["MKRN2",] > mean(expDatop["MKRN2",]), 1, 0)
table(MKRN2pif)
## MKRN2pif
## 0 1
## 410 381
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ MKRN2pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("MKRN2 high", "MKRN2 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~MKRN2pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~
## MKRN2pif)
##
## n=773, 18 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## MKRN2pif=0 402 75 90.2 2.56 5.35
## MKRN2pif=1 371 98 82.8 2.78 5.35
##
## Chisq= 5.3 on 1 degrees of freedom, p= 0.02
MKRN2nif = ifelse( expDaton["MKRN2",] > mean(expDaton["MKRN2",]), 1, 0)
table(MKRN2nif)
## MKRN2nif
## 0 1
## 25 17
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ MKRN2nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MKRN2 high", "MKRN2 low"), fill = c('red', 'blue'))
PARP3pif = ifelse( expDatop["PARP3",] > mean(expDatop["PARP3",]), 1, 0)
table(PARP3pif)
## PARP3pif
## 0 1
## 405 386
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ PARP3pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("PARP3 high", "PARP3 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~PARP3pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## PARP3pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## PARP3pif=0 298 83 75 0.854 1.71
## PARP3pif=1 284 67 75 0.854 1.71
##
## Chisq= 1.7 on 1 degrees of freedom, p= 0.2
PARP3nif = ifelse( expDaton["PARP3",] > mean(expDaton["PARP3",]), 1, 0)
table(PARP3nif)
## PARP3nif
## 0 1
## 18 24
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ PARP3nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PARP3 high", "PARP3 low"), fill = c('red', 'blue'))
DHRS12pif = ifelse( expDatop["DHRS12",] > mean(expDatop["DHRS12",]), 1, 0)
table(DHRS12pif)
## DHRS12pif
## 0 1
## 414 377
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ DHRS12pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("DHRS12 high", "DHRS12 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~DHRS12pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~
## DHRS12pif)
##
## n=773, 18 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## DHRS12pif=0 410 99 90.2 0.851 1.78
## DHRS12pif=1 363 74 82.8 0.928 1.78
##
## Chisq= 1.8 on 1 degrees of freedom, p= 0.2
DHRS12nif = ifelse( expDaton["DHRS12",] > mean(expDaton["DHRS12",]), 1, 0)
table(DHRS12nif)
## DHRS12nif
## 0 1
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ DHRS12nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("DHRS12 high", "DHRS12 low"), fill = c('red', 'blue'))
CXCL13nif
## GSM79117 GSM79148 GSM79191 GSM79195 GSM79239 GSM79259 GSM79274
## 1 1 1 1 1 0 0
## GSM79292 GSM79341 GSM79351 GSM107082 GSM107131 GSM107166 GSM107183
## 1 1 1 1 1 0 1
## OXF5431 OXF5432 OXF5440 OXF5444 OXF5448 OXF5451 OXF5460
## 0 0 0 0 1 0 1
## OXF5466 GSM50045 GSM50048 GSM50054 GSM50060 GSM50061 GSM50066
## 1 0 0 1 1 1 0
## GSM50071 GSM50093 GSM50116 1639356696 1639355859 1639356632 1639357580
## 0 0 0 0 1 1 1
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162
## 0 1 1 1 1 0 0
FBXO34pif = ifelse( expDatop["FBXO34",] > mean(expDatop["FBXO34",]), 1, 0)
table(FBXO34pif)
## FBXO34pif
## 0 1
## 388 403
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ FBXO34pif ),
xlab = "Time in months", ylab = "Metastasis-free survival proportion", col = c(2,4))
legend('topright', c("FBXO34 high", "FBXO34 low"), fill = c('red', 'blue'))
survdiff( Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~FBXO34pif )
## Call:
## survdiff(formula = Surv(sampleDataop$dfsTime, sampleDataop$dfsEvent) ~
## FBXO34pif)
##
## n=582, 209 observations deleted due to missingness.
##
## N Observed Expected (O-E)^2/E (O-E)^2/V
## FBXO34pif=0 289 70 76.2 0.502 1.02
## FBXO34pif=1 293 80 73.8 0.518 1.02
##
## Chisq= 1 on 1 degrees of freedom, p= 0.3
FBXO34nif = ifelse( expDaton["FBXO34",] > mean(expDaton["FBXO34",]), 1, 0)
table(FBXO34nif)
## FBXO34nif
## 0 1
## 21 21
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ FBXO34nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("FBXO34 high", "FBXO34 low"), fill = c('red', 'blue'))
CXCL13nif
## GSM79117 GSM79148 GSM79191 GSM79195 GSM79239 GSM79259 GSM79274
## 1 1 1 1 1 0 0
## GSM79292 GSM79341 GSM79351 GSM107082 GSM107131 GSM107166 GSM107183
## 1 1 1 1 1 0 1
## OXF5431 OXF5432 OXF5440 OXF5444 OXF5448 OXF5451 OXF5460
## 0 0 0 0 1 0 1
## OXF5466 GSM50045 GSM50048 GSM50054 GSM50060 GSM50061 GSM50066
## 1 0 0 1 1 1 0
## GSM50071 GSM50093 GSM50116 1639356696 1639355859 1639356632 1639357580
## 0 0 0 0 1 1 1
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162
## 0 1 1 1 1 0 0
IL21pif = ifelse( expDatop["IL21",] > mean(expDatop["IL21",]), 1, 0)
table(IL21pif)
## IL21pif
## 0 1
## 430 361
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ IL21pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IL21 high", "IL21 low"), fill = c('red', 'blue'))
IL21nif = ifelse( expDaton["IL21",] > mean(expDaton["IL21",]), 1, 0)
table(IL21nif)
## IL21nif
## 0 1
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ IL21nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("IL21 high", "IL21 low"), fill = c('red', 'blue'))
CXCL13nif
## GSM79117 GSM79148 GSM79191 GSM79195 GSM79239 GSM79259 GSM79274
## 1 1 1 1 1 0 0
## GSM79292 GSM79341 GSM79351 GSM107082 GSM107131 GSM107166 GSM107183
## 1 1 1 1 1 0 1
## OXF5431 OXF5432 OXF5440 OXF5444 OXF5448 OXF5451 OXF5460
## 0 0 0 0 1 0 1
## OXF5466 GSM50045 GSM50048 GSM50054 GSM50060 GSM50061 GSM50066
## 1 0 0 1 1 1 0
## GSM50071 GSM50093 GSM50116 1639356696 1639355859 1639356632 1639357580
## 0 0 0 0 1 1 1
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162
## 0 1 1 1 1 0 0
PTNpif = ifelse( expDatop["PTN",] > mean(expDatop["PTN",]), 1, 0)
table(PTNpif)
## PTNpif
## 0 1
## 511 280
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ PTNpif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PTN high", "PTN low"), fill = c('red', 'blue'))
PTNnif = ifelse( expDaton["PTN",] > mean(expDaton["PTN",]), 1, 0)
table(PTNnif)
## PTNnif
## 0 1
## 31 11
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ PTNnif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("PTN high", "PTN low"), fill = c('red', 'blue'))
SLC4A1pif = ifelse( expDatop["SLC4A1",] > mean(expDatop["SLC4A1",]), 1, 0)
table(SLC4A1pif)
## SLC4A1pif
## 0 1
## 430 361
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ SLC4A1pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("SLC4A1 high", "SLC4A1 low"), fill = c('red', 'blue'))
SLC4A1nif = ifelse( expDaton["SLC4A1",] > mean(expDaton["SLC4A1",]), 1, 0)
table(SLC4A1nif)
## SLC4A1nif
## 0 1
## 23 19
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ SLC4A1nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("SLC4A1 high", "SLC4A1 low"), fill = c('red', 'blue'))
MBpif = ifelse( expDatop["MB",] > mean(expDatop["MB",]), 1, 0)
table(MBpif)
## MBpif
## 0 1
## 411 380
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ MBpif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MB high", "MB low"), fill = c('red', 'blue'))
MBnif = ifelse( expDaton["MB",] > mean(expDaton["MB",]), 1, 0)
table(MBnif)
## MBnif
## 0 1
## 24 18
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ MBnif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("MB high", "MB low"), fill = c('red', 'blue'))
KIR2DL4pif = ifelse( expDatop["KIR2DL4",] > mean(expDatop["KIR2DL4",]), 1, 0)
table(KIR2DL4pif)
## KIR2DL4pif
## 0 1
## 412 379
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ KIR2DL4pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("KIR2DL4 high", "KIR2DL4 low"), fill = c('red', 'blue'))
KIR2DL4nif = ifelse( expDaton["KIR2DL4",] > mean(expDaton["KIR2DL4",]), 1, 0)
table(KIR2DL4nif)
## KIR2DL4nif
## 0 1
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ KIR2DL4nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("KIR2DL4 high", "KIR2DL4 low"), fill = c('red', 'blue'))
CD247pif = ifelse( expDatop["CD247",] > mean(expDatop["CD247",]), 1, 0)
table(CD247pif)
## CD247pif
## 0 1
## 477 314
plot( survfit( Surv(sampleDataop$dssTime, sampleDataop$dssEvent) ~ CD247pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CD247 high", "CD247 low"), fill = c('red', 'blue'))
CD247nif = ifelse( expDaton["CD247",] > mean(expDaton["CD247",]), 1, 0)
table(CD247nif)
## CD247nif
## 0 1
## 23 19
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CD247nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CD247 high", "CXCL13 low"), fill = c('red', 'blue'))
CREG1pif = ifelse( expDatop["CREG1",] > mean(expDatop["CREG1",]), 1, 0)
table(CREG1pif)
## CREG1pif
## 0 1
## 367 424
plot( survfit( Surv(sampleDataop$dmfsTime, sampleDataop$dmfsEvent) ~ CREG1pif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CREG1 high", "CREG1 low"), fill = c('red', 'blue'))
CREG1nif = ifelse( expDaton["CREG1",] > mean(expDaton["CREG1",]), 1, 0)
table(CREG1nif)
## CREG1nif
## 0 1
## 22 20
plot( survfit( Surv(sampleDataon$dssTime, sampleDataon$dssEvent) ~ CREG1nif ),
xlab = "Time in months", ylab = "Survival proportion", col = c(2,4))
legend('topright', c("CREG1 high", "CREG1 low"), fill = c('red', 'blue'))
CXCL13nif
## GSM79117 GSM79148 GSM79191 GSM79195 GSM79239 GSM79259 GSM79274
## 1 1 1 1 1 0 0
## GSM79292 GSM79341 GSM79351 GSM107082 GSM107131 GSM107166 GSM107183
## 1 1 1 1 1 0 1
## OXF5431 OXF5432 OXF5440 OXF5444 OXF5448 OXF5451 OXF5460
## 0 0 0 0 1 0 1
## OXF5466 GSM50045 GSM50048 GSM50054 GSM50060 GSM50061 GSM50066
## 1 0 0 1 1 1 0
## GSM50071 GSM50093 GSM50116 1639356696 1639355859 1639356632 1639357580
## 0 0 0 0 1 1 1
## 1639355773 1639357556 1639356846 1639358104 1639355985 1639356292 1639357162
## 0 1 1 1 1 0 0